Multiple sequence alignment - TraesCS7D01G330100

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G330100 chr7D 100.000 5267 0 0 1 5267 421794168 421788902 0.000000e+00 9727.0
1 TraesCS7D01G330100 chr7D 80.142 141 20 7 4068 4207 541495975 541496108 1.210000e-16 99.0
2 TraesCS7D01G330100 chr7D 86.047 86 10 2 4123 4207 540792152 540792068 2.020000e-14 91.6
3 TraesCS7D01G330100 chr7D 78.571 140 22 7 4069 4207 540715228 540715096 9.400000e-13 86.1
4 TraesCS7D01G330100 chr7D 80.851 94 14 4 2000 2091 421409975 421409884 2.630000e-08 71.3
5 TraesCS7D01G330100 chr7B 91.397 2848 149 45 1939 4736 439417283 439420084 0.000000e+00 3814.0
6 TraesCS7D01G330100 chr7B 87.613 1873 112 48 1 1836 439415439 439417228 0.000000e+00 2063.0
7 TraesCS7D01G330100 chr7B 80.142 141 20 7 4068 4207 585488084 585488217 1.210000e-16 99.0
8 TraesCS7D01G330100 chr7B 85.882 85 12 0 4123 4207 584268999 584268915 2.020000e-14 91.6
9 TraesCS7D01G330100 chr7B 78.472 144 22 8 4066 4207 584035744 584035608 9.400000e-13 86.1
10 TraesCS7D01G330100 chr7B 80.851 94 14 4 2000 2091 437672881 437672790 2.630000e-08 71.3
11 TraesCS7D01G330100 chr7A 86.946 1287 94 34 1563 2795 511496580 511497846 0.000000e+00 1378.0
12 TraesCS7D01G330100 chr7A 86.175 1179 77 40 3599 4724 511498771 511499916 0.000000e+00 1195.0
13 TraesCS7D01G330100 chr7A 85.569 887 63 36 708 1551 511495740 511496604 0.000000e+00 869.0
14 TraesCS7D01G330100 chr7A 88.542 672 45 9 2858 3509 511497887 511498546 0.000000e+00 785.0
15 TraesCS7D01G330100 chr7A 89.357 451 43 4 4820 5267 511499930 511500378 3.560000e-156 562.0
16 TraesCS7D01G330100 chr7A 81.944 504 42 24 26 494 511495082 511495571 1.070000e-101 381.0
17 TraesCS7D01G330100 chr7A 78.723 141 22 7 4068 4207 624808554 624808687 2.610000e-13 87.9
18 TraesCS7D01G330100 chr7A 79.808 104 15 6 1988 2088 511714473 511714573 2.630000e-08 71.3
19 TraesCS7D01G330100 chr6D 79.468 263 40 10 5011 5267 381192331 381192585 1.950000e-39 174.0
20 TraesCS7D01G330100 chr6D 80.240 167 25 5 5100 5260 440224175 440224339 9.270000e-23 119.0
21 TraesCS7D01G330100 chr4D 77.597 308 55 13 4961 5267 134761453 134761159 1.950000e-39 174.0
22 TraesCS7D01G330100 chr4B 77.492 311 55 12 4961 5267 194036495 194036196 7.010000e-39 172.0
23 TraesCS7D01G330100 chr6B 80.383 209 36 5 5011 5219 569366513 569366310 2.540000e-33 154.0
24 TraesCS7D01G330100 chr6B 80.240 167 25 5 5100 5260 665446446 665446610 9.270000e-23 119.0
25 TraesCS7D01G330100 chr2D 81.657 169 30 1 5004 5172 28881012 28881179 7.110000e-29 139.0
26 TraesCS7D01G330100 chr2D 80.000 160 23 7 1097 1253 92736706 92736859 5.580000e-20 110.0
27 TraesCS7D01G330100 chr2D 77.114 201 38 4 5070 5267 500685366 500685561 5.580000e-20 110.0
28 TraesCS7D01G330100 chr5A 86.400 125 15 2 4941 5064 436877590 436877713 9.200000e-28 135.0
29 TraesCS7D01G330100 chr5A 87.611 113 11 3 4945 5055 512461398 512461509 1.540000e-25 128.0
30 TraesCS7D01G330100 chr5A 86.087 115 14 2 4942 5055 436828741 436828854 7.160000e-24 122.0
31 TraesCS7D01G330100 chr5A 80.838 167 22 8 1095 1253 495028806 495028642 7.160000e-24 122.0
32 TraesCS7D01G330100 chr1D 88.393 112 12 1 4945 5055 47638090 47637979 3.310000e-27 134.0
33 TraesCS7D01G330100 chrUn 86.607 112 12 3 4946 5055 33427123 33427233 2.580000e-23 121.0
34 TraesCS7D01G330100 chrUn 86.607 112 12 3 4946 5055 33489362 33489472 2.580000e-23 121.0
35 TraesCS7D01G330100 chr2B 80.000 160 23 7 1097 1253 144021271 144021424 5.580000e-20 110.0
36 TraesCS7D01G330100 chr2B 88.095 84 10 0 1170 1253 143952400 143952483 3.360000e-17 100.0
37 TraesCS7D01G330100 chr3D 80.667 150 19 9 5004 5149 346649062 346649205 2.010000e-19 108.0
38 TraesCS7D01G330100 chr3D 77.005 187 33 8 2003 2184 110245085 110244904 1.210000e-16 99.0
39 TraesCS7D01G330100 chr3D 88.462 78 9 0 1176 1253 110310830 110310753 1.560000e-15 95.3
40 TraesCS7D01G330100 chr3A 92.105 76 6 0 1178 1253 120296216 120296291 2.010000e-19 108.0
41 TraesCS7D01G330100 chr3A 75.936 187 35 8 2003 2184 120223851 120224032 2.610000e-13 87.9
42 TraesCS7D01G330100 chr5D 78.698 169 22 11 1095 1253 391854999 391854835 3.360000e-17 100.0
43 TraesCS7D01G330100 chr4A 88.710 62 7 0 4764 4825 708430373 708430434 5.660000e-10 76.8
44 TraesCS7D01G330100 chr1A 87.500 64 7 1 4763 4825 583176037 583175974 7.320000e-09 73.1
45 TraesCS7D01G330100 chr5B 83.544 79 8 3 5194 5267 526954086 526954164 9.460000e-08 69.4
46 TraesCS7D01G330100 chr5B 85.294 68 5 3 5194 5256 527011234 527011301 1.220000e-06 65.8
47 TraesCS7D01G330100 chr5B 82.278 79 9 3 5194 5267 526987836 526987914 4.400000e-06 63.9
48 TraesCS7D01G330100 chr2A 86.885 61 8 0 4765 4825 51492953 51492893 9.460000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G330100 chr7D 421788902 421794168 5266 True 9727.000000 9727 100.000000 1 5267 1 chr7D.!!$R2 5266
1 TraesCS7D01G330100 chr7B 439415439 439420084 4645 False 2938.500000 3814 89.505000 1 4736 2 chr7B.!!$F2 4735
2 TraesCS7D01G330100 chr7A 511495082 511500378 5296 False 861.666667 1378 86.422167 26 5267 6 chr7A.!!$F3 5241

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
602 664 0.107897 ATTCATGGCGCGTAACCTGA 60.108 50.0 8.43 4.77 0.00 3.86 F
854 917 0.179045 GGCACACACTTCACCTCACT 60.179 55.0 0.00 0.00 0.00 3.41 F
1888 2039 0.243365 GATTGACCACGCCATTGCAA 59.757 50.0 0.00 0.00 37.32 4.08 F
2234 2399 0.389757 CCGAGCCTCTTAGCCCTTAC 59.610 60.0 0.00 0.00 0.00 2.34 F
2450 2622 0.458669 ACGGCGTCGAGGTATGAAAT 59.541 50.0 20.03 0.00 40.11 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1567 1688 0.610174 CTGGTTGAGTAGGAGCAGCA 59.390 55.000 0.00 0.00 35.01 4.41 R
2708 2895 0.774908 ATCTCCCCACCGGTTTTTCA 59.225 50.000 2.97 0.00 0.00 2.69 R
3262 3472 0.107848 ACATGGGCCGCTACACTAAC 60.108 55.000 0.00 0.00 0.00 2.34 R
4040 4429 1.080298 GTGCTGAAACCTGCCATGC 60.080 57.895 0.00 0.00 0.00 4.06 R
4402 4802 1.056103 CTCAACGAACAGACTGAGCG 58.944 55.000 10.08 13.95 30.82 5.03 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.073199 ACAGGGGCGAAGACAAAGG 59.927 57.895 0.00 0.00 37.00 3.11
94 106 4.814294 CCGAGTCGAAAGCCCGGG 62.814 72.222 19.09 19.09 36.81 5.73
172 202 0.179134 CAAGACGACGACAGGGATCC 60.179 60.000 1.92 1.92 0.00 3.36
185 215 0.672401 GGGATCCGTGCTGTCGAAAA 60.672 55.000 5.45 0.00 0.00 2.29
186 216 1.153353 GGATCCGTGCTGTCGAAAAA 58.847 50.000 0.00 0.00 0.00 1.94
187 217 1.737793 GGATCCGTGCTGTCGAAAAAT 59.262 47.619 0.00 0.00 0.00 1.82
249 290 4.379243 CGTGAAGAGCCGTGCCCT 62.379 66.667 0.00 0.00 0.00 5.19
270 315 4.443266 GAGCGAGCTTGGACGGCT 62.443 66.667 2.37 0.00 43.26 5.52
313 358 4.041198 TCCGGTTAATAATGGTGGAGGATC 59.959 45.833 0.00 0.00 0.00 3.36
314 359 4.202419 CCGGTTAATAATGGTGGAGGATCA 60.202 45.833 0.00 0.00 36.25 2.92
315 360 4.755123 CGGTTAATAATGGTGGAGGATCAC 59.245 45.833 0.00 0.00 36.25 3.06
327 378 1.230497 GGATCACCGGGAGAGAGGA 59.770 63.158 6.32 0.00 0.00 3.71
330 381 1.289982 ATCACCGGGAGAGAGGAGGA 61.290 60.000 6.32 0.00 0.00 3.71
332 383 2.197324 CCGGGAGAGAGGAGGAGG 59.803 72.222 0.00 0.00 0.00 4.30
337 388 0.930726 GGAGAGAGGAGGAGGAGGAA 59.069 60.000 0.00 0.00 0.00 3.36
396 448 4.761739 TGATCAACACCAGGAATGAGAAAC 59.238 41.667 0.00 0.00 0.00 2.78
397 449 3.138304 TCAACACCAGGAATGAGAAACG 58.862 45.455 0.00 0.00 0.00 3.60
519 581 2.829741 AAGTCCACTTCTCAGCAGTC 57.170 50.000 0.00 0.00 0.00 3.51
526 588 1.342819 ACTTCTCAGCAGTCCACACTC 59.657 52.381 0.00 0.00 0.00 3.51
528 590 0.178950 TCTCAGCAGTCCACACTCCT 60.179 55.000 0.00 0.00 0.00 3.69
531 593 0.247736 CAGCAGTCCACACTCCTACC 59.752 60.000 0.00 0.00 0.00 3.18
532 594 0.115349 AGCAGTCCACACTCCTACCT 59.885 55.000 0.00 0.00 0.00 3.08
533 595 1.358103 AGCAGTCCACACTCCTACCTA 59.642 52.381 0.00 0.00 0.00 3.08
534 596 1.477295 GCAGTCCACACTCCTACCTAC 59.523 57.143 0.00 0.00 0.00 3.18
535 597 2.803956 CAGTCCACACTCCTACCTACA 58.196 52.381 0.00 0.00 0.00 2.74
599 661 1.937899 AGTAATTCATGGCGCGTAACC 59.062 47.619 8.43 0.00 0.00 2.85
602 664 0.107897 ATTCATGGCGCGTAACCTGA 60.108 50.000 8.43 4.77 0.00 3.86
664 726 2.290008 ACCTGCACGGATGTACATTGAA 60.290 45.455 10.30 0.00 36.31 2.69
700 763 2.853731 TTTTTGGTTGCGGTACTGTG 57.146 45.000 3.10 0.00 0.00 3.66
755 818 4.936248 CGAGAGCGAGCGAGCGAG 62.936 72.222 1.41 0.00 43.00 5.03
762 825 3.021788 GAGCGAGCGAGCGTCATC 61.022 66.667 0.00 0.00 43.00 2.92
849 912 2.591715 AGCGGCACACACTTCACC 60.592 61.111 1.45 0.00 0.00 4.02
850 913 2.591715 GCGGCACACACTTCACCT 60.592 61.111 0.00 0.00 0.00 4.00
854 917 0.179045 GGCACACACTTCACCTCACT 60.179 55.000 0.00 0.00 0.00 3.41
919 1006 6.183347 CACAAGTAAAGGATCCCATCTTTCT 58.817 40.000 8.55 0.00 35.22 2.52
925 1012 3.586429 AGGATCCCATCTTTCTCTCTCC 58.414 50.000 8.55 0.00 0.00 3.71
927 1014 2.182516 TCCCATCTTTCTCTCTCCCC 57.817 55.000 0.00 0.00 0.00 4.81
937 1024 1.230650 TCTCTCCCCCTCTCTCCCA 60.231 63.158 0.00 0.00 0.00 4.37
985 1072 2.359602 CACCCACAGCAGCCAGAG 60.360 66.667 0.00 0.00 0.00 3.35
986 1073 4.341783 ACCCACAGCAGCCAGAGC 62.342 66.667 0.00 0.00 40.32 4.09
987 1074 4.340246 CCCACAGCAGCCAGAGCA 62.340 66.667 0.00 0.00 43.56 4.26
988 1075 2.746671 CCACAGCAGCCAGAGCAG 60.747 66.667 0.00 0.00 43.56 4.24
1031 1118 2.202676 CCTGCTTCTCGTCCTCGC 60.203 66.667 0.00 0.00 36.96 5.03
1156 1243 3.781307 TCGACGGCATCCCCAAGG 61.781 66.667 0.00 0.00 0.00 3.61
1253 1340 0.798776 GTCGTCGACTTCCTCGGTAA 59.201 55.000 18.09 0.00 43.16 2.85
1260 1347 2.489329 CGACTTCCTCGGTAACTACCAA 59.511 50.000 6.71 0.00 46.80 3.67
1282 1370 1.225983 CTCCTCTCCTCTCTCGCCA 59.774 63.158 0.00 0.00 0.00 5.69
1364 1484 2.358247 TCGCCTTGCCGTCCTTTC 60.358 61.111 0.00 0.00 0.00 2.62
1373 1494 0.686769 GCCGTCCTTTCCCTCTCCTA 60.687 60.000 0.00 0.00 0.00 2.94
1390 1511 5.003804 TCTCCTATTCTTCTTTTGGTGCAC 58.996 41.667 8.80 8.80 0.00 4.57
1394 1515 2.057137 TCTTCTTTTGGTGCACTGCT 57.943 45.000 17.98 0.00 0.00 4.24
1395 1516 2.378038 TCTTCTTTTGGTGCACTGCTT 58.622 42.857 17.98 0.00 0.00 3.91
1396 1517 3.550820 TCTTCTTTTGGTGCACTGCTTA 58.449 40.909 17.98 0.00 0.00 3.09
1429 1550 0.730265 TTTGCGTTGCGATATCCCAC 59.270 50.000 0.00 0.00 0.00 4.61
1455 1576 5.613358 AATGTCTCTGTTTCTAAAAGCGG 57.387 39.130 0.00 0.00 0.00 5.52
1514 1635 4.326826 TCTGACCTTGGTCATGATGAAAC 58.673 43.478 21.09 0.00 32.39 2.78
1551 1672 0.610687 GCTGCTCCTACTCAACCAGT 59.389 55.000 0.00 0.00 39.41 4.00
1559 1680 3.764434 TCCTACTCAACCAGTGTCTCATC 59.236 47.826 0.00 0.00 36.43 2.92
1567 1688 5.070446 TCAACCAGTGTCTCATCTTTAGTGT 59.930 40.000 0.00 0.00 0.00 3.55
1603 1724 5.827797 TCAACCAGCTAGAGTGTTCAAAAAT 59.172 36.000 0.00 0.00 0.00 1.82
1660 1787 1.608717 GCCCGAGCTCTCCTTTCAGA 61.609 60.000 12.85 0.00 35.50 3.27
1661 1788 0.459489 CCCGAGCTCTCCTTTCAGAG 59.541 60.000 12.85 0.00 42.68 3.35
1662 1789 1.468985 CCGAGCTCTCCTTTCAGAGA 58.531 55.000 12.85 0.00 42.44 3.10
1663 1790 1.821753 CCGAGCTCTCCTTTCAGAGAA 59.178 52.381 12.85 0.00 42.44 2.87
1664 1791 2.159254 CCGAGCTCTCCTTTCAGAGAAG 60.159 54.545 12.85 0.00 42.44 2.85
1805 1953 6.209589 GCTCCTTTTCTTTTCCCTCTGTAAAT 59.790 38.462 0.00 0.00 0.00 1.40
1876 2027 1.237285 ACTGCTGCAACCGATTGACC 61.237 55.000 3.02 0.00 38.15 4.02
1888 2039 0.243365 GATTGACCACGCCATTGCAA 59.757 50.000 0.00 0.00 37.32 4.08
1889 2040 0.678395 ATTGACCACGCCATTGCAAA 59.322 45.000 1.71 0.00 37.32 3.68
1890 2041 0.678395 TTGACCACGCCATTGCAAAT 59.322 45.000 1.71 0.00 37.32 2.32
1891 2042 1.539157 TGACCACGCCATTGCAAATA 58.461 45.000 1.71 0.00 37.32 1.40
1892 2043 1.889170 TGACCACGCCATTGCAAATAA 59.111 42.857 1.71 0.00 37.32 1.40
1895 2046 1.660104 CCACGCCATTGCAAATAAAGC 59.340 47.619 1.71 1.21 37.32 3.51
1896 2047 2.609350 CACGCCATTGCAAATAAAGCT 58.391 42.857 1.71 0.00 37.32 3.74
1897 2048 3.428725 CCACGCCATTGCAAATAAAGCTA 60.429 43.478 1.71 0.00 37.32 3.32
1900 2051 3.551485 CGCCATTGCAAATAAAGCTAACC 59.449 43.478 1.71 0.00 37.32 2.85
1901 2052 4.502962 GCCATTGCAAATAAAGCTAACCA 58.497 39.130 1.71 0.00 37.47 3.67
1914 2065 6.780457 AAAGCTAACCATGAATTGCTATGT 57.220 33.333 0.00 0.00 0.00 2.29
1916 2067 4.037208 AGCTAACCATGAATTGCTATGTGC 59.963 41.667 0.00 0.00 43.25 4.57
1921 2072 4.955450 ACCATGAATTGCTATGTGCCTTTA 59.045 37.500 0.00 0.00 42.00 1.85
1923 2074 6.098695 ACCATGAATTGCTATGTGCCTTTATT 59.901 34.615 0.00 0.00 42.00 1.40
1925 2076 7.811236 CCATGAATTGCTATGTGCCTTTATTAG 59.189 37.037 0.00 0.00 42.00 1.73
1926 2077 6.738114 TGAATTGCTATGTGCCTTTATTAGC 58.262 36.000 0.00 0.00 42.00 3.09
1927 2078 4.811555 TTGCTATGTGCCTTTATTAGCG 57.188 40.909 0.00 0.00 42.00 4.26
1928 2079 4.066646 TGCTATGTGCCTTTATTAGCGA 57.933 40.909 0.00 0.00 42.00 4.93
1929 2080 4.447290 TGCTATGTGCCTTTATTAGCGAA 58.553 39.130 0.00 0.00 42.00 4.70
1932 2094 5.049405 GCTATGTGCCTTTATTAGCGAACAT 60.049 40.000 0.00 0.00 31.84 2.71
1945 2107 1.393539 GCGAACATCACGTTGTATGCT 59.606 47.619 8.64 0.00 38.19 3.79
1952 2114 4.388773 ACATCACGTTGTATGCTGTGTAAG 59.611 41.667 0.00 0.00 34.08 2.34
1956 2118 5.050634 TCACGTTGTATGCTGTGTAAGTTTC 60.051 40.000 0.00 0.00 34.08 2.78
1957 2119 4.812091 ACGTTGTATGCTGTGTAAGTTTCA 59.188 37.500 0.00 0.00 0.00 2.69
1963 2125 8.439993 TGTATGCTGTGTAAGTTTCACTTTTA 57.560 30.769 13.02 0.00 39.51 1.52
1964 2126 8.339714 TGTATGCTGTGTAAGTTTCACTTTTAC 58.660 33.333 13.02 9.86 39.51 2.01
1966 2128 6.781138 TGCTGTGTAAGTTTCACTTTTACTG 58.219 36.000 13.02 1.35 39.51 2.74
1967 2129 6.596106 TGCTGTGTAAGTTTCACTTTTACTGA 59.404 34.615 13.02 0.00 39.51 3.41
1968 2130 7.282224 TGCTGTGTAAGTTTCACTTTTACTGAT 59.718 33.333 13.02 0.00 39.51 2.90
2010 2175 3.880846 GAGCATTTCGGGCTGCCG 61.881 66.667 13.40 8.37 42.78 5.69
2234 2399 0.389757 CCGAGCCTCTTAGCCCTTAC 59.610 60.000 0.00 0.00 0.00 2.34
2250 2415 4.576463 GCCCTTACTGAAATGTGATACAGG 59.424 45.833 0.00 0.00 35.08 4.00
2253 2418 3.652057 ACTGAAATGTGATACAGGGGG 57.348 47.619 0.00 0.00 35.08 5.40
2450 2622 0.458669 ACGGCGTCGAGGTATGAAAT 59.541 50.000 20.03 0.00 40.11 2.17
2454 2626 2.548067 GGCGTCGAGGTATGAAATCCAT 60.548 50.000 7.01 0.00 39.25 3.41
2456 2628 3.059884 CGTCGAGGTATGAAATCCATGG 58.940 50.000 4.97 4.97 36.71 3.66
2457 2629 3.243737 CGTCGAGGTATGAAATCCATGGA 60.244 47.826 18.88 18.88 36.71 3.41
2458 2630 4.310769 GTCGAGGTATGAAATCCATGGAG 58.689 47.826 21.33 1.59 36.71 3.86
2459 2631 3.324846 TCGAGGTATGAAATCCATGGAGG 59.675 47.826 21.33 0.00 36.71 4.30
2485 2657 3.262405 ACCTTGGCGTTAGAAATGTAGGA 59.738 43.478 0.00 0.00 0.00 2.94
2506 2678 2.181125 TGACCTTGGCATTGCATCATT 58.819 42.857 11.39 0.00 0.00 2.57
2508 2680 3.008157 TGACCTTGGCATTGCATCATTTT 59.992 39.130 11.39 0.00 0.00 1.82
2509 2681 4.004982 GACCTTGGCATTGCATCATTTTT 58.995 39.130 11.39 0.00 0.00 1.94
2511 2683 4.937015 ACCTTGGCATTGCATCATTTTTAC 59.063 37.500 11.39 0.00 0.00 2.01
2512 2684 4.936411 CCTTGGCATTGCATCATTTTTACA 59.064 37.500 11.39 0.00 0.00 2.41
2513 2685 5.064198 CCTTGGCATTGCATCATTTTTACAG 59.936 40.000 11.39 0.00 0.00 2.74
2514 2686 5.149973 TGGCATTGCATCATTTTTACAGT 57.850 34.783 11.39 0.00 0.00 3.55
2721 2908 2.642700 CGGCTGAAAAACCGGTGG 59.357 61.111 8.52 0.00 45.74 4.61
2747 2934 1.983119 GATCAGGGGGCACGGATTCA 61.983 60.000 0.00 0.00 0.00 2.57
2774 2964 2.224843 TGCTCTGGAATTGCCTTGAGAA 60.225 45.455 13.11 3.14 38.98 2.87
2824 3014 9.793245 CTCGGTATCAAAATATATGACGTTTTC 57.207 33.333 0.00 0.00 0.00 2.29
2903 3094 1.174783 AGTAGGTAGGCACAGTGTCG 58.825 55.000 1.61 0.00 0.00 4.35
3055 3258 6.440328 ACATTTGCAGACATTAAAATAGGGGT 59.560 34.615 0.00 0.00 0.00 4.95
3115 3318 3.959943 GAGAATCTTCTGACTAGGCGAC 58.040 50.000 0.00 0.00 37.73 5.19
3121 3324 3.439476 TCTTCTGACTAGGCGACTAACAC 59.561 47.826 0.00 0.00 43.83 3.32
3180 3385 2.181426 TTTTTCGCCGGCATAAATCG 57.819 45.000 28.98 8.23 0.00 3.34
3184 3389 2.052237 GCCGGCATAAATCGCACG 60.052 61.111 24.80 0.00 0.00 5.34
3262 3472 4.578871 TCCACAGTACATCAGATTGTTGG 58.421 43.478 0.00 0.00 0.00 3.77
3352 3585 2.360165 GCATGGCTGGTAAAGAAGATGG 59.640 50.000 0.00 0.00 0.00 3.51
3534 3832 6.423042 GTTCTCTGCTGAACTAGTTTGAAAC 58.577 40.000 10.02 0.00 42.03 2.78
3535 3833 5.670485 TCTCTGCTGAACTAGTTTGAAACA 58.330 37.500 10.02 1.67 0.00 2.83
3536 3834 6.291377 TCTCTGCTGAACTAGTTTGAAACAT 58.709 36.000 10.02 0.00 0.00 2.71
3537 3835 7.441836 TCTCTGCTGAACTAGTTTGAAACATA 58.558 34.615 10.02 0.00 0.00 2.29
3538 3836 7.385205 TCTCTGCTGAACTAGTTTGAAACATAC 59.615 37.037 10.02 0.00 0.00 2.39
3540 3838 7.171508 TCTGCTGAACTAGTTTGAAACATACAG 59.828 37.037 10.02 9.76 0.00 2.74
3541 3839 6.765989 TGCTGAACTAGTTTGAAACATACAGT 59.234 34.615 10.02 5.05 0.00 3.55
3542 3840 7.929245 TGCTGAACTAGTTTGAAACATACAGTA 59.071 33.333 10.02 5.80 0.00 2.74
3543 3841 8.221766 GCTGAACTAGTTTGAAACATACAGTAC 58.778 37.037 10.02 0.00 0.00 2.73
3544 3842 9.477484 CTGAACTAGTTTGAAACATACAGTACT 57.523 33.333 10.02 0.00 0.00 2.73
3545 3843 9.826574 TGAACTAGTTTGAAACATACAGTACTT 57.173 29.630 10.02 0.00 0.00 2.24
3554 3852 9.826574 TTGAAACATACAGTACTTTACTTGTCT 57.173 29.630 0.00 0.00 36.76 3.41
3558 3856 8.874744 ACATACAGTACTTTACTTGTCTAGGA 57.125 34.615 0.00 0.00 36.76 2.94
3562 3860 8.418597 ACAGTACTTTACTTGTCTAGGATTGA 57.581 34.615 0.00 0.00 36.76 2.57
3580 3955 5.915196 GGATTGAAAGTAGTTTTGCACACTC 59.085 40.000 0.84 0.00 0.00 3.51
3595 3970 0.950836 CACTCCGTGAATGCAAACCA 59.049 50.000 0.00 0.00 35.23 3.67
3606 3981 1.284657 TGCAAACCAAAACGTGCATG 58.715 45.000 3.82 3.82 41.85 4.06
3640 4017 7.852945 GCGAATTTTGATAGTCTTACCTCATTG 59.147 37.037 0.00 0.00 0.00 2.82
3652 4029 7.763985 AGTCTTACCTCATTGTTTTTGGTTTTG 59.236 33.333 0.00 0.00 32.74 2.44
3928 4305 4.323477 TTTGTCGTCAGCCCCGGG 62.323 66.667 15.80 15.80 0.00 5.73
3972 4349 2.816672 TCCAAAGTTGCACGCATCATAA 59.183 40.909 3.15 0.00 0.00 1.90
4033 4422 5.181748 GTGGCATGATCTAACTGAAGAACT 58.818 41.667 0.00 0.00 0.00 3.01
4040 4429 4.252971 TCTAACTGAAGAACTTGACGGG 57.747 45.455 0.00 0.00 0.00 5.28
4063 4452 2.949106 CAGGTTTCAGCACGGCAG 59.051 61.111 0.00 0.00 0.00 4.85
4267 4656 1.486310 CTCCCCCGATCATGAAGTGAA 59.514 52.381 0.00 0.00 40.97 3.18
4302 4702 2.493278 AGCCCTGTATGTACGTAACGTT 59.507 45.455 5.88 5.88 41.54 3.99
4305 4705 3.504863 CCTGTATGTACGTAACGTTGCT 58.495 45.455 11.99 2.40 41.54 3.91
4328 4728 1.134220 TGCTGCTGCTGATGATGATGA 60.134 47.619 17.00 0.00 40.48 2.92
4394 4794 7.094890 GCTGGAGATGTTAAGTTATGATGATGG 60.095 40.741 0.00 0.00 0.00 3.51
4406 4806 6.428159 AGTTATGATGATGGGTAAAATCGCTC 59.572 38.462 0.00 0.00 0.00 5.03
4424 4824 2.287909 GCTCAGTCTGTTCGTTGAGAGT 60.288 50.000 0.00 0.00 39.46 3.24
4455 4855 3.921677 CCGTGCCGGTATAGATATGTTT 58.078 45.455 1.90 0.00 42.73 2.83
4590 4998 2.223203 GCAAGAGGATCAGAATTGTGCG 60.223 50.000 0.00 0.00 37.82 5.34
4634 5044 1.737355 GCCTGCACTGCTGTTTTCCA 61.737 55.000 1.98 0.00 0.00 3.53
4663 5091 2.991190 CTCCATTTGCACAGAACAATGC 59.009 45.455 1.72 0.00 42.40 3.56
4687 5117 2.611292 GGCTGTAATGACTCTGCATGAC 59.389 50.000 0.00 0.00 31.42 3.06
4710 5140 2.539688 CGCATGCAGAATTAAGCGTCTA 59.460 45.455 19.57 0.00 40.25 2.59
4723 5153 0.992802 GCGTCTAGCCTTCGTTTGAG 59.007 55.000 0.00 0.00 40.81 3.02
4738 5168 3.599704 GAGGGGCCGCGTACGTAT 61.600 66.667 17.90 0.00 37.70 3.06
4739 5169 2.203337 AGGGGCCGCGTACGTATA 60.203 61.111 17.90 0.00 37.70 1.47
4740 5170 1.795170 GAGGGGCCGCGTACGTATAA 61.795 60.000 17.90 0.00 37.70 0.98
4741 5171 1.181098 AGGGGCCGCGTACGTATAAT 61.181 55.000 17.90 0.00 37.70 1.28
4742 5172 0.525761 GGGGCCGCGTACGTATAATA 59.474 55.000 17.90 0.00 37.70 0.98
4743 5173 1.067915 GGGGCCGCGTACGTATAATAA 60.068 52.381 17.90 0.00 37.70 1.40
4744 5174 2.253603 GGGCCGCGTACGTATAATAAG 58.746 52.381 17.90 0.00 37.70 1.73
4745 5175 2.095263 GGGCCGCGTACGTATAATAAGA 60.095 50.000 17.90 0.00 37.70 2.10
4746 5176 3.564511 GGCCGCGTACGTATAATAAGAA 58.435 45.455 17.90 0.00 37.70 2.52
4747 5177 3.980775 GGCCGCGTACGTATAATAAGAAA 59.019 43.478 17.90 0.00 37.70 2.52
4748 5178 4.089065 GGCCGCGTACGTATAATAAGAAAG 59.911 45.833 17.90 0.00 37.70 2.62
4749 5179 4.911610 GCCGCGTACGTATAATAAGAAAGA 59.088 41.667 17.90 0.00 37.70 2.52
4750 5180 5.570589 GCCGCGTACGTATAATAAGAAAGAT 59.429 40.000 17.90 0.00 37.70 2.40
4751 5181 6.742718 GCCGCGTACGTATAATAAGAAAGATA 59.257 38.462 17.90 0.00 37.70 1.98
4752 5182 7.271223 GCCGCGTACGTATAATAAGAAAGATAA 59.729 37.037 17.90 0.00 37.70 1.75
4753 5183 8.783251 CCGCGTACGTATAATAAGAAAGATAAG 58.217 37.037 17.90 0.00 37.70 1.73
4754 5184 9.533983 CGCGTACGTATAATAAGAAAGATAAGA 57.466 33.333 17.90 0.00 33.53 2.10
4815 5245 2.051879 ATCGAGATGATACAACCGCG 57.948 50.000 0.00 0.00 34.83 6.46
4817 5247 1.121240 CGAGATGATACAACCGCGTC 58.879 55.000 4.92 0.00 0.00 5.19
4819 5249 0.821517 AGATGATACAACCGCGTCCA 59.178 50.000 4.92 0.00 0.00 4.02
4820 5250 1.206132 AGATGATACAACCGCGTCCAA 59.794 47.619 4.92 0.00 0.00 3.53
4821 5251 2.004017 GATGATACAACCGCGTCCAAA 58.996 47.619 4.92 0.00 0.00 3.28
4822 5252 1.434555 TGATACAACCGCGTCCAAAG 58.565 50.000 4.92 0.00 0.00 2.77
4823 5253 1.001068 TGATACAACCGCGTCCAAAGA 59.999 47.619 4.92 0.00 0.00 2.52
4824 5254 2.070783 GATACAACCGCGTCCAAAGAA 58.929 47.619 4.92 0.00 0.00 2.52
4825 5255 1.219646 TACAACCGCGTCCAAAGAAC 58.780 50.000 4.92 0.00 0.00 3.01
4826 5256 0.745128 ACAACCGCGTCCAAAGAACA 60.745 50.000 4.92 0.00 0.00 3.18
4827 5257 0.591170 CAACCGCGTCCAAAGAACAT 59.409 50.000 4.92 0.00 0.00 2.71
4828 5258 1.001815 CAACCGCGTCCAAAGAACATT 60.002 47.619 4.92 0.00 0.00 2.71
4829 5259 0.591170 ACCGCGTCCAAAGAACATTG 59.409 50.000 4.92 0.00 0.00 2.82
4830 5260 0.871722 CCGCGTCCAAAGAACATTGA 59.128 50.000 4.92 0.00 31.84 2.57
4831 5261 1.265635 CCGCGTCCAAAGAACATTGAA 59.734 47.619 4.92 0.00 31.84 2.69
4832 5262 2.095263 CCGCGTCCAAAGAACATTGAAT 60.095 45.455 4.92 0.00 31.84 2.57
4833 5263 3.564511 CGCGTCCAAAGAACATTGAATT 58.435 40.909 0.00 0.00 31.84 2.17
4834 5264 3.361644 CGCGTCCAAAGAACATTGAATTG 59.638 43.478 0.00 0.00 31.84 2.32
4835 5265 4.545610 GCGTCCAAAGAACATTGAATTGA 58.454 39.130 0.00 0.00 31.84 2.57
4836 5266 4.981674 GCGTCCAAAGAACATTGAATTGAA 59.018 37.500 0.00 0.00 31.84 2.69
4837 5267 5.634859 GCGTCCAAAGAACATTGAATTGAAT 59.365 36.000 0.00 0.00 31.84 2.57
4838 5268 6.146021 GCGTCCAAAGAACATTGAATTGAATT 59.854 34.615 0.00 0.00 31.84 2.17
4839 5269 7.503991 CGTCCAAAGAACATTGAATTGAATTG 58.496 34.615 0.00 0.00 31.84 2.32
4840 5270 7.381948 CGTCCAAAGAACATTGAATTGAATTGA 59.618 33.333 0.00 0.00 31.84 2.57
4841 5271 9.211485 GTCCAAAGAACATTGAATTGAATTGAT 57.789 29.630 0.00 0.00 31.84 2.57
4863 5293 9.999660 TTGATATATTAAGGTAATACAACCGCA 57.000 29.630 0.00 0.00 44.77 5.69
4870 5300 8.789825 TTAAGGTAATACAACCGCATCTAAAA 57.210 30.769 0.00 0.00 44.77 1.52
4890 5320 0.322816 AATGCCCGGCCTATGCATAG 60.323 55.000 24.33 24.33 44.49 2.23
4893 5323 1.672356 CCCGGCCTATGCATAGCAC 60.672 63.158 25.60 19.13 43.04 4.40
4895 5325 1.006220 CGGCCTATGCATAGCACGA 60.006 57.895 29.16 3.83 43.04 4.35
4921 5351 3.766591 ACAAATCCAACAAGTCCAACACA 59.233 39.130 0.00 0.00 0.00 3.72
4928 5358 2.175202 ACAAGTCCAACACAGCCAAAA 58.825 42.857 0.00 0.00 0.00 2.44
4930 5360 2.929398 CAAGTCCAACACAGCCAAAAAC 59.071 45.455 0.00 0.00 0.00 2.43
4943 5373 6.638873 CACAGCCAAAAACAAACATCGTATTA 59.361 34.615 0.00 0.00 0.00 0.98
5009 5440 9.866655 TTCTGCCAATAGATTATTGTAAATCCT 57.133 29.630 7.74 0.00 43.05 3.24
5023 5454 4.901849 TGTAAATCCTAGAGACCCATGAGG 59.098 45.833 0.00 0.00 43.78 3.86
5034 5465 1.469335 CCCATGAGGCCCATTCATGC 61.469 60.000 22.23 0.00 46.68 4.06
5049 5480 0.108992 CATGCATGACAAGGTGGTGC 60.109 55.000 22.59 0.00 36.39 5.01
5079 5510 3.309582 CACACCCCGCTAGTGGAT 58.690 61.111 24.31 8.56 39.63 3.41
5081 5512 0.104304 CACACCCCGCTAGTGGATAC 59.896 60.000 24.31 0.00 39.63 2.24
5083 5514 1.216175 ACACCCCGCTAGTGGATACTA 59.784 52.381 24.31 0.00 39.63 1.82
5095 5526 3.976654 AGTGGATACTATGTGAGGCCAAT 59.023 43.478 5.01 0.00 34.74 3.16
5138 5569 6.166279 CACATACCACTAAGAGCTTGAGAAA 58.834 40.000 0.00 0.00 0.00 2.52
5165 5596 2.930385 ATACATGCGCGCTCCTGCTT 62.930 55.000 33.29 14.07 36.97 3.91
5188 5619 4.107051 GCCACGCCTCACACATGC 62.107 66.667 0.00 0.00 0.00 4.06
5191 5622 1.588824 CCACGCCTCACACATGCATT 61.589 55.000 0.00 0.00 0.00 3.56
5192 5623 0.455464 CACGCCTCACACATGCATTG 60.455 55.000 0.00 1.69 0.00 2.82
5208 5639 2.762472 CATTGTGTTTCGTGATCGAGC 58.238 47.619 0.00 0.00 46.81 5.03
5219 5650 3.723235 GATCGAGCCAAGCCGAGCA 62.723 63.158 9.65 0.00 37.49 4.26
5223 5654 3.612247 GAGCCAAGCCGAGCAAGGA 62.612 63.158 1.32 0.00 0.00 3.36
5241 5672 1.138266 GGACCTATGCCACGTGTATGT 59.862 52.381 15.65 3.64 0.00 2.29
5260 5691 7.329226 GTGTATGTGCTGCTTTATTTTTGTCAT 59.671 33.333 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.280119 GTCCAGTGTCTGCGCACA 60.280 61.111 5.66 0.00 41.52 4.57
5 6 2.280119 TGTCCAGTGTCTGCGCAC 60.280 61.111 5.66 0.00 39.51 5.34
37 38 0.517316 ATCGCGCAACCTTTGTCTTC 59.483 50.000 8.75 0.00 0.00 2.87
47 48 0.454452 GTTTCCCTGAATCGCGCAAC 60.454 55.000 8.75 0.00 0.00 4.17
91 103 1.067250 CCCATTAAATTGGCGCCCG 59.933 57.895 26.77 1.52 35.29 6.13
92 104 1.227527 GCCCATTAAATTGGCGCCC 60.228 57.895 26.77 6.44 35.08 6.13
93 105 4.436515 GCCCATTAAATTGGCGCC 57.563 55.556 22.73 22.73 35.08 6.53
96 108 1.205893 TGAACCGCCCATTAAATTGGC 59.794 47.619 0.00 0.00 41.85 4.52
97 109 3.258228 GTTGAACCGCCCATTAAATTGG 58.742 45.455 0.00 0.00 36.46 3.16
98 110 3.919216 TGTTGAACCGCCCATTAAATTG 58.081 40.909 0.00 0.00 0.00 2.32
99 111 4.282195 TCTTGTTGAACCGCCCATTAAATT 59.718 37.500 0.00 0.00 0.00 1.82
100 112 3.829601 TCTTGTTGAACCGCCCATTAAAT 59.170 39.130 0.00 0.00 0.00 1.40
101 113 3.223435 TCTTGTTGAACCGCCCATTAAA 58.777 40.909 0.00 0.00 0.00 1.52
199 229 1.596477 GAGCTCCCATCCATGTCGC 60.596 63.158 0.87 0.00 0.00 5.19
249 290 1.664649 CGTCCAAGCTCGCTCACAA 60.665 57.895 0.00 0.00 0.00 3.33
313 358 1.454847 CTCCTCCTCTCTCCCGGTG 60.455 68.421 0.00 0.00 0.00 4.94
314 359 2.695970 CCTCCTCCTCTCTCCCGGT 61.696 68.421 0.00 0.00 0.00 5.28
315 360 2.197324 CCTCCTCCTCTCTCCCGG 59.803 72.222 0.00 0.00 0.00 5.73
316 361 1.150536 CTCCTCCTCCTCTCTCCCG 59.849 68.421 0.00 0.00 0.00 5.14
327 378 0.417841 TGCTACCCTTTCCTCCTCCT 59.582 55.000 0.00 0.00 0.00 3.69
330 381 0.547712 TGCTGCTACCCTTTCCTCCT 60.548 55.000 0.00 0.00 0.00 3.69
332 383 1.488393 AGATGCTGCTACCCTTTCCTC 59.512 52.381 0.00 0.00 0.00 3.71
337 388 4.506271 CCATAATGAGATGCTGCTACCCTT 60.506 45.833 0.00 0.00 0.00 3.95
397 449 4.509737 GACCCGGTACTGGCGAGC 62.510 72.222 15.96 0.10 35.55 5.03
519 581 1.203994 CGGTTGTAGGTAGGAGTGTGG 59.796 57.143 0.00 0.00 0.00 4.17
526 588 2.444421 ACAGAGACGGTTGTAGGTAGG 58.556 52.381 0.00 0.00 0.00 3.18
528 590 3.489355 TGAACAGAGACGGTTGTAGGTA 58.511 45.455 0.00 0.00 0.00 3.08
531 593 4.082733 TGAGATGAACAGAGACGGTTGTAG 60.083 45.833 0.00 0.00 0.00 2.74
532 594 3.824443 TGAGATGAACAGAGACGGTTGTA 59.176 43.478 0.00 0.00 0.00 2.41
533 595 2.628178 TGAGATGAACAGAGACGGTTGT 59.372 45.455 0.00 0.00 0.00 3.32
534 596 3.057245 TCTGAGATGAACAGAGACGGTTG 60.057 47.826 0.00 0.00 39.10 3.77
535 597 3.057174 GTCTGAGATGAACAGAGACGGTT 60.057 47.826 0.00 0.00 43.58 4.44
599 661 1.179152 TGCCAAATGTGCAGGATCAG 58.821 50.000 0.00 0.00 34.05 2.90
602 664 1.855295 TCATGCCAAATGTGCAGGAT 58.145 45.000 6.99 0.00 43.73 3.24
656 718 2.163412 GCGGCAAATCCTGTTCAATGTA 59.837 45.455 0.00 0.00 0.00 2.29
664 726 0.387565 AAAAACGCGGCAAATCCTGT 59.612 45.000 12.47 0.00 0.00 4.00
700 763 2.100216 CATAAGCAACCGCGCCAC 59.900 61.111 0.00 0.00 45.49 5.01
712 775 4.202010 CGGCCCAACTGATTTAACCATAAG 60.202 45.833 0.00 0.00 0.00 1.73
750 813 4.194720 GACCGGATGACGCTCGCT 62.195 66.667 9.46 0.00 42.52 4.93
751 814 3.774959 ATGACCGGATGACGCTCGC 62.775 63.158 9.46 0.00 42.52 5.03
752 815 1.946156 CATGACCGGATGACGCTCG 60.946 63.158 9.46 0.00 42.52 5.03
753 816 2.240500 GCATGACCGGATGACGCTC 61.241 63.158 9.46 0.00 42.52 5.03
754 817 2.202932 GCATGACCGGATGACGCT 60.203 61.111 9.46 0.00 42.52 5.07
755 818 3.272334 GGCATGACCGGATGACGC 61.272 66.667 9.46 3.47 42.52 5.19
919 1006 1.230650 TGGGAGAGAGGGGGAGAGA 60.231 63.158 0.00 0.00 0.00 3.10
925 1012 2.284921 TGCTGTGGGAGAGAGGGG 60.285 66.667 0.00 0.00 0.00 4.79
927 1014 0.107800 CATGTGCTGTGGGAGAGAGG 60.108 60.000 0.00 0.00 0.00 3.69
986 1073 4.492160 CCATTGCTGCCGCTGCTG 62.492 66.667 21.13 12.76 38.71 4.41
987 1074 4.728110 TCCATTGCTGCCGCTGCT 62.728 61.111 21.13 1.23 38.71 4.24
988 1075 4.189188 CTCCATTGCTGCCGCTGC 62.189 66.667 14.83 14.83 36.97 5.25
989 1076 4.189188 GCTCCATTGCTGCCGCTG 62.189 66.667 0.70 0.00 36.97 5.18
990 1077 4.728110 TGCTCCATTGCTGCCGCT 62.728 61.111 0.70 0.00 36.97 5.52
991 1078 3.480225 GATGCTCCATTGCTGCCGC 62.480 63.158 0.00 0.00 0.00 6.53
992 1079 2.719979 GATGCTCCATTGCTGCCG 59.280 61.111 0.00 0.00 0.00 5.69
993 1080 2.719979 CGATGCTCCATTGCTGCC 59.280 61.111 0.00 0.00 0.00 4.85
1253 1340 3.791545 AGAGGAGAGGAGAGATTGGTAGT 59.208 47.826 0.00 0.00 0.00 2.73
1260 1347 1.072331 GCGAGAGAGGAGAGGAGAGAT 59.928 57.143 0.00 0.00 0.00 2.75
1349 1469 3.062466 GGGAAAGGACGGCAAGGC 61.062 66.667 0.00 0.00 0.00 4.35
1352 1472 1.677552 GAGAGGGAAAGGACGGCAA 59.322 57.895 0.00 0.00 0.00 4.52
1364 1484 5.189180 CACCAAAAGAAGAATAGGAGAGGG 58.811 45.833 0.00 0.00 0.00 4.30
1373 1494 2.961062 AGCAGTGCACCAAAAGAAGAAT 59.039 40.909 19.20 0.00 0.00 2.40
1390 1511 6.144402 CGCAAAGCCCATAAAATAATAAGCAG 59.856 38.462 0.00 0.00 0.00 4.24
1394 1515 6.256757 GCAACGCAAAGCCCATAAAATAATAA 59.743 34.615 0.00 0.00 0.00 1.40
1395 1516 5.751028 GCAACGCAAAGCCCATAAAATAATA 59.249 36.000 0.00 0.00 0.00 0.98
1396 1517 4.570369 GCAACGCAAAGCCCATAAAATAAT 59.430 37.500 0.00 0.00 0.00 1.28
1446 1567 3.501950 GCTCCAAATCAACCGCTTTTAG 58.498 45.455 0.00 0.00 0.00 1.85
1448 1569 1.000843 GGCTCCAAATCAACCGCTTTT 59.999 47.619 0.00 0.00 0.00 2.27
1455 1576 3.800628 GCTGTGGCTCCAAATCAAC 57.199 52.632 0.00 0.00 35.22 3.18
1514 1635 3.059325 GCAGCACACTAAACAAGAGTCAG 60.059 47.826 0.00 0.00 0.00 3.51
1551 1672 3.007290 AGCAGCACACTAAAGATGAGACA 59.993 43.478 0.00 0.00 0.00 3.41
1559 1680 3.056536 TGAGTAGGAGCAGCACACTAAAG 60.057 47.826 0.00 0.00 0.00 1.85
1567 1688 0.610174 CTGGTTGAGTAGGAGCAGCA 59.390 55.000 0.00 0.00 35.01 4.41
1603 1724 7.218228 TGATTAGCTTTGCATCAAGAGAAAA 57.782 32.000 2.23 0.00 0.00 2.29
1648 1775 7.441017 TCTTCTTTTCTTCTCTGAAAGGAGAG 58.559 38.462 2.72 0.00 41.03 3.20
1660 1787 7.978975 CCACTCGATTCTATCTTCTTTTCTTCT 59.021 37.037 0.00 0.00 0.00 2.85
1661 1788 7.762159 ACCACTCGATTCTATCTTCTTTTCTTC 59.238 37.037 0.00 0.00 0.00 2.87
1662 1789 7.616313 ACCACTCGATTCTATCTTCTTTTCTT 58.384 34.615 0.00 0.00 0.00 2.52
1663 1790 7.176589 ACCACTCGATTCTATCTTCTTTTCT 57.823 36.000 0.00 0.00 0.00 2.52
1664 1791 8.928270 TTACCACTCGATTCTATCTTCTTTTC 57.072 34.615 0.00 0.00 0.00 2.29
1805 1953 5.884322 TCCGGTCTGCTTTAGGAGTATATA 58.116 41.667 0.00 0.00 34.87 0.86
1837 1985 5.634020 GCAGTAAATCACGAGTACTTTGAGT 59.366 40.000 12.26 8.01 0.00 3.41
1838 1986 5.864474 AGCAGTAAATCACGAGTACTTTGAG 59.136 40.000 12.26 1.87 0.00 3.02
1839 1987 5.633601 CAGCAGTAAATCACGAGTACTTTGA 59.366 40.000 9.81 9.81 0.00 2.69
1840 1988 5.668866 GCAGCAGTAAATCACGAGTACTTTG 60.669 44.000 0.00 0.00 0.00 2.77
1843 1991 3.056821 TGCAGCAGTAAATCACGAGTACT 60.057 43.478 0.00 0.00 0.00 2.73
1844 1992 3.250744 TGCAGCAGTAAATCACGAGTAC 58.749 45.455 0.00 0.00 0.00 2.73
1845 1993 3.586100 TGCAGCAGTAAATCACGAGTA 57.414 42.857 0.00 0.00 0.00 2.59
1846 1994 2.455674 TGCAGCAGTAAATCACGAGT 57.544 45.000 0.00 0.00 0.00 4.18
1847 1995 2.159653 GGTTGCAGCAGTAAATCACGAG 60.160 50.000 2.05 0.00 0.00 4.18
1849 1997 1.464023 CGGTTGCAGCAGTAAATCACG 60.464 52.381 2.05 0.00 0.00 4.35
1876 2027 2.609350 AGCTTTATTTGCAATGGCGTG 58.391 42.857 0.00 0.00 45.35 5.34
1888 2039 8.917088 ACATAGCAATTCATGGTTAGCTTTATT 58.083 29.630 0.00 0.00 40.93 1.40
1889 2040 8.355169 CACATAGCAATTCATGGTTAGCTTTAT 58.645 33.333 0.00 0.00 40.93 1.40
1890 2041 7.681782 GCACATAGCAATTCATGGTTAGCTTTA 60.682 37.037 0.00 0.00 44.79 1.85
1891 2042 6.567050 CACATAGCAATTCATGGTTAGCTTT 58.433 36.000 0.00 0.26 40.93 3.51
1892 2043 5.450965 GCACATAGCAATTCATGGTTAGCTT 60.451 40.000 0.00 0.00 44.79 3.74
1914 2065 3.308595 CGTGATGTTCGCTAATAAAGGCA 59.691 43.478 0.00 0.00 0.00 4.75
1916 2067 5.163893 ACAACGTGATGTTCGCTAATAAAGG 60.164 40.000 0.00 0.00 39.29 3.11
1921 2072 4.260212 GCATACAACGTGATGTTCGCTAAT 60.260 41.667 0.00 0.00 39.29 1.73
1923 2074 2.601314 GCATACAACGTGATGTTCGCTA 59.399 45.455 0.00 0.00 39.29 4.26
1925 2076 1.393539 AGCATACAACGTGATGTTCGC 59.606 47.619 0.00 2.43 39.29 4.70
1926 2077 2.411748 ACAGCATACAACGTGATGTTCG 59.588 45.455 0.00 0.00 42.96 3.95
1927 2078 3.186409 ACACAGCATACAACGTGATGTTC 59.814 43.478 0.00 0.00 42.96 3.18
1928 2079 3.138304 ACACAGCATACAACGTGATGTT 58.862 40.909 0.00 0.00 42.96 2.71
1929 2080 2.766313 ACACAGCATACAACGTGATGT 58.234 42.857 0.00 0.00 46.06 3.06
1932 2094 3.985008 ACTTACACAGCATACAACGTGA 58.015 40.909 0.00 0.00 33.56 4.35
1952 2114 7.454260 AAGATCCCATCAGTAAAAGTGAAAC 57.546 36.000 0.00 0.00 30.32 2.78
1956 2118 9.177608 TGATAAAAGATCCCATCAGTAAAAGTG 57.822 33.333 0.00 0.00 0.00 3.16
1957 2119 9.753674 TTGATAAAAGATCCCATCAGTAAAAGT 57.246 29.630 0.00 0.00 0.00 2.66
1963 2125 7.124599 TGCAAATTGATAAAAGATCCCATCAGT 59.875 33.333 0.00 0.00 0.00 3.41
1964 2126 7.494211 TGCAAATTGATAAAAGATCCCATCAG 58.506 34.615 0.00 0.00 0.00 2.90
1966 2128 6.423001 GCTGCAAATTGATAAAAGATCCCATC 59.577 38.462 0.00 0.00 0.00 3.51
1967 2129 6.285990 GCTGCAAATTGATAAAAGATCCCAT 58.714 36.000 0.00 0.00 0.00 4.00
1968 2130 5.395546 GGCTGCAAATTGATAAAAGATCCCA 60.396 40.000 0.50 0.00 0.00 4.37
2227 2392 4.576463 CCTGTATCACATTTCAGTAAGGGC 59.424 45.833 0.00 0.00 0.00 5.19
2234 2399 3.200825 AGACCCCCTGTATCACATTTCAG 59.799 47.826 0.00 0.00 0.00 3.02
2250 2415 3.181454 TGAAACTCTGAACTTGAGACCCC 60.181 47.826 0.00 0.00 35.66 4.95
2253 2418 7.475840 ACAAAATGAAACTCTGAACTTGAGAC 58.524 34.615 0.00 0.00 35.66 3.36
2454 2626 1.488705 AACGCCAAGGTCATCCTCCA 61.489 55.000 0.00 0.00 44.35 3.86
2456 2628 1.480954 TCTAACGCCAAGGTCATCCTC 59.519 52.381 0.00 0.00 44.35 3.71
2458 2630 2.396590 TTCTAACGCCAAGGTCATCC 57.603 50.000 0.00 0.00 0.00 3.51
2459 2631 3.689649 ACATTTCTAACGCCAAGGTCATC 59.310 43.478 0.00 0.00 0.00 2.92
2460 2632 3.686016 ACATTTCTAACGCCAAGGTCAT 58.314 40.909 0.00 0.00 0.00 3.06
2461 2633 3.134574 ACATTTCTAACGCCAAGGTCA 57.865 42.857 0.00 0.00 0.00 4.02
2462 2634 3.621715 CCTACATTTCTAACGCCAAGGTC 59.378 47.826 0.00 0.00 0.00 3.85
2464 2636 3.869065 TCCTACATTTCTAACGCCAAGG 58.131 45.455 0.00 0.00 0.00 3.61
2465 2637 5.006746 GTCATCCTACATTTCTAACGCCAAG 59.993 44.000 0.00 0.00 0.00 3.61
2470 2642 5.523916 CCAAGGTCATCCTACATTTCTAACG 59.476 44.000 0.00 0.00 44.35 3.18
2472 2644 5.045213 TGCCAAGGTCATCCTACATTTCTAA 60.045 40.000 0.00 0.00 44.35 2.10
2485 2657 1.855295 TGATGCAATGCCAAGGTCAT 58.145 45.000 1.53 0.00 0.00 3.06
2506 2678 6.766944 TGGATTTTCTACGGTTGACTGTAAAA 59.233 34.615 4.53 5.55 37.27 1.52
2508 2680 5.856156 TGGATTTTCTACGGTTGACTGTAA 58.144 37.500 4.53 0.00 37.27 2.41
2509 2681 5.471556 TGGATTTTCTACGGTTGACTGTA 57.528 39.130 3.05 3.05 36.70 2.74
2511 2683 4.377022 CGTTGGATTTTCTACGGTTGACTG 60.377 45.833 0.00 0.00 0.00 3.51
2512 2684 3.744426 CGTTGGATTTTCTACGGTTGACT 59.256 43.478 0.00 0.00 0.00 3.41
2513 2685 3.120442 CCGTTGGATTTTCTACGGTTGAC 60.120 47.826 9.08 0.00 46.25 3.18
2514 2686 3.068560 CCGTTGGATTTTCTACGGTTGA 58.931 45.455 9.08 0.00 46.25 3.18
2542 2714 3.951037 TCTACTTTTGCCATGTGTGTGTT 59.049 39.130 0.00 0.00 0.00 3.32
2708 2895 0.774908 ATCTCCCCACCGGTTTTTCA 59.225 50.000 2.97 0.00 0.00 2.69
2721 2908 1.771746 TGCCCCCTGATCATCTCCC 60.772 63.158 0.00 0.00 0.00 4.30
2747 2934 1.377725 CAATTCCAGAGCACGGCCT 60.378 57.895 0.00 0.00 0.00 5.19
2774 2964 4.344390 GGAGTAGAACCGAAATCCATAGGT 59.656 45.833 0.00 0.00 38.88 3.08
2843 3033 9.442033 CCGGGAATAAAAATATAAGACGTTTTC 57.558 33.333 0.00 0.00 0.00 2.29
2862 3052 6.197903 ACTAACTAAACTACTACCCGGGAAT 58.802 40.000 32.02 14.63 0.00 3.01
2864 3054 5.193099 ACTAACTAAACTACTACCCGGGA 57.807 43.478 32.02 10.31 0.00 5.14
2865 3055 5.532779 CCTACTAACTAAACTACTACCCGGG 59.467 48.000 22.25 22.25 0.00 5.73
3115 3318 9.084164 AGTATAACAATAGCAGTTTCGTGTTAG 57.916 33.333 0.00 0.00 35.56 2.34
3121 3324 6.903883 ACCAGTATAACAATAGCAGTTTCG 57.096 37.500 0.00 0.00 0.00 3.46
3184 3389 5.292834 CCATGGCATCACGAATATGTATCTC 59.707 44.000 0.00 0.00 0.00 2.75
3262 3472 0.107848 ACATGGGCCGCTACACTAAC 60.108 55.000 0.00 0.00 0.00 2.34
3352 3585 5.535333 CCATGCACATAAAAGATGATTCCC 58.465 41.667 0.00 0.00 0.00 3.97
3510 3808 6.037172 TGTTTCAAACTAGTTCAGCAGAGAAC 59.963 38.462 8.95 8.20 46.35 3.01
3531 3829 9.924650 CCTAGACAAGTAAAGTACTGTATGTTT 57.075 33.333 0.00 0.00 39.39 2.83
3532 3830 9.305555 TCCTAGACAAGTAAAGTACTGTATGTT 57.694 33.333 0.00 0.00 39.39 2.71
3536 3834 9.524496 TCAATCCTAGACAAGTAAAGTACTGTA 57.476 33.333 0.00 0.00 39.39 2.74
3537 3835 8.418597 TCAATCCTAGACAAGTAAAGTACTGT 57.581 34.615 0.00 0.00 39.39 3.55
3538 3836 9.706691 TTTCAATCCTAGACAAGTAAAGTACTG 57.293 33.333 0.00 0.00 39.39 2.74
3540 3838 9.708092 ACTTTCAATCCTAGACAAGTAAAGTAC 57.292 33.333 0.00 0.00 34.02 2.73
3542 3840 9.930693 CTACTTTCAATCCTAGACAAGTAAAGT 57.069 33.333 0.00 0.00 38.04 2.66
3543 3841 9.930693 ACTACTTTCAATCCTAGACAAGTAAAG 57.069 33.333 0.00 0.00 0.00 1.85
3547 3845 9.057089 CAAAACTACTTTCAATCCTAGACAAGT 57.943 33.333 0.00 0.00 0.00 3.16
3548 3846 8.017946 GCAAAACTACTTTCAATCCTAGACAAG 58.982 37.037 0.00 0.00 0.00 3.16
3551 3849 7.041372 TGTGCAAAACTACTTTCAATCCTAGAC 60.041 37.037 0.00 0.00 0.00 2.59
3552 3850 6.995686 TGTGCAAAACTACTTTCAATCCTAGA 59.004 34.615 0.00 0.00 0.00 2.43
3553 3851 7.041098 AGTGTGCAAAACTACTTTCAATCCTAG 60.041 37.037 1.50 0.00 27.55 3.02
3554 3852 6.770785 AGTGTGCAAAACTACTTTCAATCCTA 59.229 34.615 1.50 0.00 27.55 2.94
3555 3853 5.594317 AGTGTGCAAAACTACTTTCAATCCT 59.406 36.000 1.50 0.00 27.55 3.24
3558 3856 5.505654 CGGAGTGTGCAAAACTACTTTCAAT 60.506 40.000 10.49 0.00 31.60 2.57
3560 3858 3.311322 CGGAGTGTGCAAAACTACTTTCA 59.689 43.478 10.49 0.00 31.60 2.69
3561 3859 3.311596 ACGGAGTGTGCAAAACTACTTTC 59.688 43.478 10.49 0.00 42.51 2.62
3562 3860 3.275999 ACGGAGTGTGCAAAACTACTTT 58.724 40.909 10.49 0.00 42.51 2.66
3580 3955 1.520590 CGTTTTGGTTTGCATTCACGG 59.479 47.619 0.00 0.00 0.00 4.94
3615 3991 8.883731 ACAATGAGGTAAGACTATCAAAATTCG 58.116 33.333 0.00 0.00 0.00 3.34
3640 4017 9.838975 ATCAATTTCTGAAACAAAACCAAAAAC 57.161 25.926 4.73 0.00 37.67 2.43
3652 4029 5.091431 CCAAGCTCGATCAATTTCTGAAAC 58.909 41.667 4.73 0.00 37.67 2.78
3928 4305 6.073003 GGATCCATCTTCACATACCGAATTTC 60.073 42.308 6.95 0.00 0.00 2.17
4033 4422 2.992817 AAACCTGCCATGCCCGTCAA 62.993 55.000 0.00 0.00 0.00 3.18
4040 4429 1.080298 GTGCTGAAACCTGCCATGC 60.080 57.895 0.00 0.00 0.00 4.06
4242 4631 2.142761 CATGATCGGGGGAGAGGCA 61.143 63.158 0.00 0.00 0.00 4.75
4267 4656 2.582636 ACAGGGCTAACCATCTGGATTT 59.417 45.455 2.55 0.00 43.89 2.17
4305 4705 1.077716 ATCATCAGCAGCAGCAGCA 60.078 52.632 12.92 0.00 45.49 4.41
4328 4728 1.188219 CCGTCGATCCCCTCCATCAT 61.188 60.000 0.00 0.00 0.00 2.45
4394 4794 3.060895 CGAACAGACTGAGCGATTTTACC 59.939 47.826 10.08 0.00 0.00 2.85
4402 4802 1.056103 CTCAACGAACAGACTGAGCG 58.944 55.000 10.08 13.95 30.82 5.03
4406 4806 3.865745 ACAAACTCTCAACGAACAGACTG 59.134 43.478 0.00 0.00 0.00 3.51
4568 4974 3.015327 GCACAATTCTGATCCTCTTGCT 58.985 45.455 0.00 0.00 0.00 3.91
4569 4975 2.223203 CGCACAATTCTGATCCTCTTGC 60.223 50.000 0.00 0.00 0.00 4.01
4590 4998 4.944249 GGTTCAGGAAGCGCAAAC 57.056 55.556 11.47 3.77 0.00 2.93
4620 5030 1.069022 CCACGATGGAAAACAGCAGTG 60.069 52.381 0.00 0.00 40.96 3.66
4634 5044 1.001020 TGCAAATGGAGGCCACGAT 60.001 52.632 5.01 0.00 35.80 3.73
4663 5091 2.635714 TGCAGAGTCATTACAGCCATG 58.364 47.619 0.00 0.00 0.00 3.66
4687 5117 1.257586 CGCTTAATTCTGCATGCGCG 61.258 55.000 14.09 15.07 42.97 6.86
4710 5140 2.034221 GCCCCTCAAACGAAGGCT 59.966 61.111 0.00 0.00 40.57 4.58
4720 5150 2.956799 TATACGTACGCGGCCCCTCA 62.957 60.000 16.72 0.00 43.45 3.86
4723 5153 0.525761 TATTATACGTACGCGGCCCC 59.474 55.000 16.72 0.00 43.45 5.80
4797 5227 0.736636 ACGCGGTTGTATCATCTCGA 59.263 50.000 12.47 0.00 0.00 4.04
4808 5238 0.591170 ATGTTCTTTGGACGCGGTTG 59.409 50.000 12.47 0.00 0.00 3.77
4815 5245 8.592105 TCAATTCAATTCAATGTTCTTTGGAC 57.408 30.769 0.00 0.00 0.00 4.02
4837 5267 9.999660 TGCGGTTGTATTACCTTAATATATCAA 57.000 29.630 0.00 0.00 35.97 2.57
4844 5274 8.967664 TTTAGATGCGGTTGTATTACCTTAAT 57.032 30.769 0.00 0.00 35.97 1.40
4845 5275 8.789825 TTTTAGATGCGGTTGTATTACCTTAA 57.210 30.769 0.00 0.00 35.97 1.85
4846 5276 8.789825 TTTTTAGATGCGGTTGTATTACCTTA 57.210 30.769 0.00 0.00 35.97 2.69
4847 5277 7.690952 TTTTTAGATGCGGTTGTATTACCTT 57.309 32.000 0.00 0.00 35.97 3.50
4870 5300 0.112218 TATGCATAGGCCGGGCATTT 59.888 50.000 31.59 12.57 45.34 2.32
4875 5305 1.672356 GTGCTATGCATAGGCCGGG 60.672 63.158 30.14 9.57 41.91 5.73
4878 5308 1.081892 CATCGTGCTATGCATAGGCC 58.918 55.000 30.14 17.54 41.91 5.19
4890 5320 1.335780 TGTTGGATTTGTGCATCGTGC 60.336 47.619 0.00 3.44 45.29 5.34
4893 5323 3.236816 GACTTGTTGGATTTGTGCATCG 58.763 45.455 0.00 0.00 0.00 3.84
4895 5325 2.964464 TGGACTTGTTGGATTTGTGCAT 59.036 40.909 0.00 0.00 0.00 3.96
4905 5335 0.385390 GGCTGTGTTGGACTTGTTGG 59.615 55.000 0.00 0.00 0.00 3.77
4921 5351 8.085296 TCAATAATACGATGTTTGTTTTTGGCT 58.915 29.630 0.00 0.00 0.00 4.75
4994 5425 9.442047 CATGGGTCTCTAGGATTTACAATAATC 57.558 37.037 0.00 0.00 34.48 1.75
5009 5440 0.268869 ATGGGCCTCATGGGTCTCTA 59.731 55.000 4.53 0.00 40.18 2.43
5023 5454 1.202486 CCTTGTCATGCATGAATGGGC 60.202 52.381 30.24 17.80 38.75 5.36
5034 5465 0.950836 TTTCGCACCACCTTGTCATG 59.049 50.000 0.00 0.00 0.00 3.07
5049 5480 1.268625 GGGGTGTGGCTAAACTTTTCG 59.731 52.381 0.00 0.00 0.00 3.46
5079 5510 7.458397 CCCTTATAAATTGGCCTCACATAGTA 58.542 38.462 3.32 0.00 0.00 1.82
5081 5512 5.711976 CCCCTTATAAATTGGCCTCACATAG 59.288 44.000 3.32 0.00 0.00 2.23
5083 5514 4.169856 TCCCCTTATAAATTGGCCTCACAT 59.830 41.667 3.32 0.00 0.00 3.21
5183 5614 3.667695 CGATCACGAAACACAATGCATGT 60.668 43.478 0.00 0.00 42.11 3.21
5184 5615 2.841907 CGATCACGAAACACAATGCATG 59.158 45.455 0.00 0.00 42.66 4.06
5185 5616 2.741517 TCGATCACGAAACACAATGCAT 59.258 40.909 0.00 0.00 45.74 3.96
5186 5617 2.139118 TCGATCACGAAACACAATGCA 58.861 42.857 0.00 0.00 45.74 3.96
5208 5639 1.899437 TAGGTCCTTGCTCGGCTTGG 61.899 60.000 0.00 0.82 0.00 3.61
5219 5650 1.563924 TACACGTGGCATAGGTCCTT 58.436 50.000 21.57 0.00 0.00 3.36
5223 5654 1.742411 GCACATACACGTGGCATAGGT 60.742 52.381 21.57 8.31 37.37 3.08
5241 5672 4.629092 TGCATGACAAAAATAAAGCAGCA 58.371 34.783 0.00 0.00 0.00 4.41


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.